Outgoing Ombudsman Emily O'Reilly had revealed her office is investigating a large number of complaints against the Department of Social Protection.
The Office of the Ombudsman dealt with 3,412 complaints last year, slightly down on 2011.
Not all of the complaints were investigated, with the Ombudsman urging those involved in 1,453 cases to take "reasonable steps" to resolve the complaint before making a complaint to her office.
Excluding these "premature complaints", the highest number of issues raised related to the Civil Service, with most involving the Department of Social Protection.
It accounted for 624 of the 917 complaints against the Civil Service.
Some 80 complaints were made against the Department of Agriculture, Food and Marine and 78 against the Revenue Commissioners.
Local authorities accounted for 595 complaints, of which 59 were against Dublin City Council, 48 against Cork County Council and 36 against Galway County Council.
Another 413 complaints were made against the HSE.
Among the complaints dealt with against the Department of Social Protection was a case where €68,000 in pension entitlements were wrongly withheld from a widower.
The department was also found to have given the wrong advice on job seekers benefit to a man who was moving his family to Guernsey in the Channel Islands. It incorrectly assured him he would be entitled to transfer his benefit there, causing great distress to him and his family when the truth was discovered.
Ms O'Reilly said her office was increasingly discovering "a tightening" which was making it more difficult for people to claim benefits they were previously entitled to, such as the discretionary medical card.
She said officials were "applying the letter of the law" and not using their discretion.
"The cost to individuals was enormous," she said.